In their defense, can you imagine a CS person answering an email from a teenager asking if his hero is really dead any other way?
I don't think there's supposed to be any meaning to the warlord recognizing Blair other than to tell us that it's the one who tortured him earlier in the game and that this is round two. It wouldn't really make sense: they've lured him to their own destruction to capture him a second time after already intentionally letting him go with a plan that totally changes the story of the game but also it is never mentioned or alluded to in any other way? And you're ignoring the rest of the scene which is Blair finding a marine the warlord has already killed and then realizing he's in danger (but not that it's crawling above him). The alien is there defending the shield controls.
The scene is written with an intentional 'what really happened?' there which I think throws people off thinking it's to indicate Blair survived... but it's not whether Blair is captured and taken to alien space, it's whether or not he kills the warlord (now established to be something he wants revenge against) before it gets him. I think the last script direction is just 'he fires'... but it's all a mute point long term because the next thing that happens is the entire place explodes. Which we then gild with a cut back to the rest of the characters specifically saying Blair didn't make it!)
That's all to say I don't think Prophecy is intentionally including an 'out' the same way something like Star Trek II did with Spock's quickie mind meld... it's just the kind of sci fi plot that you could take in a different direction if you ever so desired, but also that's pretty much every sci fi plot ever, you can write in a clone or a transporter accident or a crazy coincidence or whatever you want. But SM2 executable bug aside, Wing Commander wasn't ever a setting built around bringing characters back for the dead.
There was also a lot of bad commentary on it back in the day which I think sticks with us in some form or another today. You had this immediate claim that Prophecy was 'supposed to be a trilogy' so of course Blair would come back... but with the benefit of hindsiight we now know that constantly-repeated 'supposed to be a trilogy' a) came from an executive producer who didn't even make it to ship day and b) referred not to some plan for a three part story they'd meticiulously developed but to the much more practical idea that they had planned to amortize the cost of developing the Vision engine over five years and three major releases. And then you had those two weirdos running all over the internet insisting they'd written the Prophecy sequels for Origin and the third one would be called RESURRECTION and... none of that was real at all. So we lived through a LOT of noise!
I think we can pretty well establish that nobody in November 1997 planned to bring Blair back, from the development team that hadn't plotted out a sequel to Mark Hamill whose quote had already priced him out of anything but a two day shoot on WCP. Once the game came out and it became a big debate you had different attempts to figure out how to bring him back in other projects (thank you for not happening, Privateer Online game where you'fight Blair clones)... but it's all war-winning Nazi super jets drawn on napkins and not anything that even made it to within a parsec of a screenwriter.
(For my part, I had wanted him to be dead because that just made the most sense for Wing Commander... but I wouldn't have minded it going in /most/ other directions (shakes fist at evil Blair clone squadron). And in 2021 I'm happy to say he /is/ alive because Pilgrim Truth said so